After a brief summary of the four main veins in the treatment of decoherence and quantum to classical transition in cosmology since the 1980s, we focus on one of these veins in the study of quantum decoherence of cosmological perturbations in inflationary universe, the case when it does not rely on any environment. This is what ‘intrinsic’ in the title refers to—a closed quantum system, consisting of a quantum field which drives inflation. The question is whether its quantum perturbations, which interact with the density contrast giving rise to structures in the universe, decohere with an inflationary expansion of the universe. A dominant view which had propagated for a quarter of a century asserts yes, based on the belief that the large squeezing of a quantum state after a duration of inflation renders the system effectively classical. This paper debunks this view by identifying the technical fault-lines in its derivations and revealing the pitfalls in its arguments which drew earlier authors to this wrong conclusion. We use a few simple quantum mechanical models to expound where the fallacy originated: The highly squeezed ellipse quadrature in phase space cannot be simplified to a line, and the Wigner function cannot be replaced by a delta function. These measures amount to taking only the leading order in the relevant parameters in seeking the semiclassical limit and ignoring the subdominant contributions where quantum features reside. Doing so violates the bounds of the Wigner function, and its wave functions possess negative eigenvalues. Moreover, the Robertson-Schrödinger uncertainty relation for a pure state is violated. For inflationary cosmological perturbations, in addition to these features, entanglement exists between the created pairs. This uniquely quantum feature cannot be easily argued away. Indeed, it could be our best hope to retroduce the quantum nature of cosmological perturbations and the trace of an inflation field. All this points to the invariant fact that a closed quantum system, even when highly squeezed, evolves unitarily without loss of coherence; quantum cosmological perturbations do not decohere by themselves.